Sample ID: Escherichia_coli_p1

Cgmlst Stats

Cgmlst Alleles

Reference to chewBBACA: Silva et al. (2018)

Contig files scan results against PubMLST typing schemes

Reference information: These results made use of the PubMLST website developed by Keith Jolley (Jolley and Maiden 2010) and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust. The typing information was obtained using: Seemann T, mlst.

Ariba

Local database motif report

This is includes both coding and non-coding sequences. The determination of which were which was performed with ariba prepareref command.

Reference to ARIBA: Hunt et al. (2017)

Resfinder motif report

Reference to Resfinder: Zankari et al. (2012)

Quast report

SNP report

MultiQC report

MultiQC report can be found here. Reference to MultiQC: Ewels et al. (2016).

References

Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047. https://doi.org/10.1093/bioinformatics/btw354.
Hunt, Martin, Alison E Mather, Leonor Sánchez-Busó, Andrew J Page, Julian Parkhill, Jacqueline A Keane, and Simon R Harris. 2017. “ARIBA: Rapid Antimicrobial Resistance Genotyping Directly from Sequencing Reads.” Journal Article. Microbial Genomics 3 (10). https://doi.org/10.1099/mgen.0.000131.
Jolley, Keith A., and Martin C. J. Maiden. 2010. “BIGSdb: Scalable Analysis of Bacterial Genome Variation at the Population Level.” BMC Bioinformatics 11 (December): 595–95. https://doi.org/10.1186/1471-2105-11-595.
Silva, Mickael, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, and João André Carriço. 2018. “chewBBACA: A Complete Suite for Gene-by-Gene Schema Creation and Strain Identification.” Journal Article. Microbial Genomics 4 (3). https://doi.org/10.1099/mgen.0.000166.
Zankari, Ea, Henrik Hasman, Salvatore Cosentino, Martin Vestergaard, Simon Rasmussen, Ole Lund, Frank M. Aarestrup, and Mette Voldby Larsen. 2012. “Identification of acquired antimicrobial resistance genes.” Journal of Antimicrobial Chemotherapy 67 (11): 2640–44. https://doi.org/10.1093/jac/dks261.